Search found 6286 matches

by ted
Wed May 03, 2006 8:37 am
Forum: Modeling networks
Topic: Attaching a synapse changes cell response in Network Builder
Replies: 5
Views: 7333

Zip up the hoc, ses, and mod files necessary to reproduce the problem
and send them to me
ted dot carnevale at yale dot edu
and I'll try to diagnose it and tell you how to fix it.
by ted
Tue May 02, 2006 2:09 pm
Forum: Modeling networks
Topic: Attaching a synapse changes cell response in Network Builder
Replies: 5
Views: 7333

Try the latest alpha version--go to
http://www.neuron.yale.edu/neuron/install/install.html
then click on the link
Snapshots of alpha versions
and select the appropriate installer for your OS. Let me know if that fixes the problem.
by ted
Tue May 02, 2006 8:36 am
Forum: The GUI
Topic: dropdown menu
Replies: 4
Views: 6408

AFAIK only the NEURON Main Menu toolbar offers dropdown menus.
by ted
Tue May 02, 2006 8:35 am
Forum: Modeling networks
Topic: Attaching a synapse changes cell response in Network Builder
Replies: 5
Views: 7333

Haven't seen this happen before. Maybe you have uncovered a bug. What version of
NEURON are you using?
by ted
Tue May 02, 2006 8:31 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How to plot the variables in pointprocesses?
Replies: 1
Views: 3038

Suffix notation varname_mechanismname is only for distributed mechanisms. Point processes are class definitions, and individual instances of a point process use dot notaion objrefname.varname to access parameters and variables. Read chapter 5 of The NEURON Book, or at least read Hines, M.L. and Carn...
by ted
Fri Apr 28, 2006 9:42 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: calcium dependent inactivation function
Replies: 13
Views: 11784

Sorry I didn't examine the code you posted on April 17 in any detail prior to today. There were far more fundamental issues at hand then, e.g. the form of the mass balance equation for calcium, whether it made sense to split the intracellular pool of calcium into different subsets according to which...
by ted
Fri Apr 28, 2006 8:09 pm
Forum: NEURON + Python
Topic: possible section syntax
Replies: 10
Views: 12054

Re: Assigning to multiple segments at once

Going a bit further, it might also be nice to be able to do: dlist = (0.1,0.2,0.3,0.4,0.2) soma.diam = dlist which would be equivalent to: for i in range(soma.nseg): soma.segments[i].diam = dlist[i] Would this syntax produce the following relationship between nseg and the variation of diam along th...
by ted
Fri Apr 28, 2006 7:58 pm
Forum: Getting started
Topic: Cathodic and anodic extracellular stimulation
Replies: 1
Views: 4373

Re: Cathodic and anodic extracellular stimulation

ssothro wrote:in order to simulate cathodic stimulation, e_extracellular should have negative values and for anodic stimulation, e_extracellular should be positive.
True.
by ted
Thu Apr 27, 2006 11:14 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Problem in opening channel builder .ses files
Replies: 4
Views: 4561

I was able to reproduce the problem with 5.8.88. It was fixed in the alpha version I picked up from the CVS repository late last week. I see that a new set of alpha version installers is now available; why don't you get one of those from http://www.neuron.yale.edu/ftp/neuron/versions/alpha/ and see ...
by ted
Thu Apr 27, 2006 10:05 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Problem in opening channel builder .ses files
Replies: 4
Views: 4561

You may have run into a bug. If so, there is a possibility that it has already been
fixed. What version of NEURON are you using?
by ted
Thu Apr 27, 2006 9:55 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How does NEURON calculate the membrane potential?
Replies: 3
Views: 9668

Units

See this item
What units does NEURON use for current, concentration, etc.?
in the FAQ list
http://www.neuron.yale.edu/neuron/faq/general-questions
by ted
Wed Apr 26, 2006 2:20 pm
Forum: Other questions
Topic: templated cells and shape name viewer
Replies: 4
Views: 4961

Not a waste of time at all. These discussions become part of the available documentation,
and very often address issues that haven't been covered elsewhere.
by ted
Wed Apr 26, 2006 12:12 pm
Forum: Other questions
Topic: templated cells and shape name viewer
Replies: 4
Views: 4961

Correct. A class definition that is written by the CellBuilder includes a public
procedure called position() that can be used to specify the location of any
cell instance. For example,

Code: Select all

objref pyr4
pyr4 = new L4pyr()
pyr4.position(10, 20, 30) // desired coords of 0 end of root section (soma)
by ted
Tue Apr 25, 2006 11:37 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How does NEURON calculate the membrane potential?
Replies: 3
Views: 9668

Re: How does NEURON calculate the membrane potential?

How does NEURON calculate the membrane potential? Numerical integration of the cable equation. See chapter 5 of The NEURON Book, or read Hines, M.L. and Carnevale, N.T. The NEURON simulation environment. In: The Handbook of Brain Theory and Neural Networks, 2nd ed, edited by M.A. Arbib. Cambridge, ...
by ted
Fri Apr 21, 2006 12:14 am
Forum: Getting started
Topic: reduced compartment model
Replies: 1
Views: 2836

The first and most important tool for reducing model complexity is judgement, guided by experience and a thorough knowledge of the experimental basis for the model in question. There have been a few papers on the topic of model simplification; you might start by reading this one: Bush, P.C. and Sejn...